An integrated multiscale imaging workflow to resolve intracellular co-pathology in human FFPE brain tissue

Multiscale and multimodal analysis of post-mortem human brain tissue is essential for improving the characterization of neurodegenerative diseases (NDDs). Brain bank repositories provide extensive collections of formalin-fixed paraffin-embedded (FFPE) tissue enabling investigation of cellular and subcellular alterations across NDDs. Although conventional and multiplex chromogenic immunohistochemistry (cIHC) support large-scale neuropathological assessment, they do not fully capture the spatial and cellular complexity. Immunofluorescence (IF) combined with confocal microscopy increases spatial resolution, but standard section thickness limits three-dimensional (3D) analysis. Here, we present a sequential, multimodal and semi-automated workflow within a unified pipeline that enhances the multiscale definition of the neuropathological signature. Using neuronal and pathological markers as technical references, we demonstrate stepwise additive spatial information across modalities: from anatomical distribution using single cIHC, to two-dimensional combinatorial detection using multiplex cIHC, and to volumetric intracellular localisation using multiplex IF on thick sections. When applied to human FFPE brain tissue, this workflow enables reproducible and scalable multiscale protein mapping. It supports consistent detection and spatial separation of multiple markers and links chromogenic pathology with high-resolution 3D fluorescence imaging, providing a practical framework for the integrated spatial analysis of neurodegenerative pathology and beyond.